Expression-system-dependent modulation of HIV-1 envelope glycoprotein antigenicity and immunogenicity.

Recombinant expression systems differ in the type of glycosylation they impart on expressed antigens such as the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins, potentially affecting their biological properties. We performed head-to-head antigenic, immunogenic and molecular profiling of two distantly related Env surface (gp120) antigens produced in different systems: (a) mammalian (293 FreeStyle cells; 293F) cells in the presence of kifunensine, which impart only high-mannose glycans; (b) insect cells (Spodoptera frugiperda, Sf9), which confer mainly paucimannosidic glycans; (c) Sf9 cells recombinant for mammalian glycosylation enzymes (Sf9 Mimic), which impart high-mannose, hybrid and complex glycans without sialic acid; and (d) 293F cells, which impart high-mannose, hybrid and complex glycans with sialic acid. Molecular models revealed a significant difference in gp120 glycan coverage between the Sf9-derived and wild-type mammalian-cell-derived material that is predicted to affect ligand binding sites proximal to glycans. Modeling of solvent-exposed surface electrostatic potentials showed that sialic acid imparts a significant negative surface charge that may influence gp120 antigenicity and immunogenicity. Gp120 expressed in systems that do not incorporate sialic acid displayed increased ligand binding to the CD4 binding and CD4-induced sites compared to those expressed in the system that do, and imparted other more subtle differences in antigenicity in a gp120 subtype-specific manner. Non-sialic-acid-containing gp120 was significantly more immunogenic than the sialylated version when administered in two different adjuvants, and induced higher titers of antibodies competing for CD4 binding site ligand-gp120 interaction. These findings suggest that non-sialic-acid-imparting systems yield gp120 immunogens with modified antigenic and immunogenic properties, considerations that should be considered when selecting expression systems for glycosylated antigens to be used for structure-function studies and for vaccine use.

Social networks: evolving graphs with memory dependent edges

The plethora, and mass take up, of digital communication tech- nologies has resulted in a wealth of interest in social network data collection and analysis in recent years. Within many such networks the interactions are transient: thus those networks evolve over time. In this paper we introduce a class of models for such networks using evolving graphs with memory dependent edges, which may appear and disappear according to their recent history. We consider time discrete and time continuous variants of the model. We consider the long term asymptotic behaviour as a function of parameters controlling the memory dependence. In particular we show that such networks may continue evolving forever, or else may quench and become static (containing immortal and/or extinct edges). This depends on the ex- istence or otherwise of certain infinite products and series involving age dependent model parameters. To test these ideas we show how model parameters may be calibrated based on limited samples of time dependent data, and we apply these concepts to three real networks: summary data on mobile phone use from a developing region; online social-business network data from China; and disaggregated mobile phone communications data from a reality mining experiment in the US. In each case we show that there is evidence for memory dependent dynamics, such as that embodied within the class of models proposed here.

The price of space: the convergence of value in use and value in exchange

This paper discusses concepts of value from the point of view of the user of the space and the counter view of the provider of the same. Land and property are factors of production. The value of the land flows from the use to which it is put, and that in turn, is dependent upon the demand (and supply) for the product or service that is produced/provided from that space. If there is a high demand for the product (at a fixed level of supply), the price will increase and the economic rent for the land/property will increase accordingly. This is the underlying paradigm of Ricardian rent theory where the supply of land is fixed and a single good is produced. In such a case the rent of land is wholly an economic rent. Economic theory generally distinguishes between two kinds of price, price of production or “value in use” (as determined by the labour theory of value), and market price or “value in exchange” (as determined by supply and demand). It is based on a coherent and consistent theory of value and price. Effectively the distinction is between what space is ‘worth’ to an individual and that space’s price of exchange in the market place. In a perfect market where any individual has access to the same information as all others in the market, price and worth should coincide. However in a market where access to information is not uniform, and where different uses compete for the same space, it is more likely that the two figures will diverge. This paper argues that the traditional reliance of valuers to use methods of comparison to determine “price” has led to an artificial divergence of “value in use” and “value in exchange”, but now such comparison are becoming more difficult due to the diversity of lettings in the market place, there will be a requirement to return to fundamentals and pay heed to the thought process of the user in assessing the worth of the space to be let.

Lighting energy saving due to the use of direct sunlight

This paper describe a simulation program, which uses Trengenza’s average room illuminance method in conjunction with hourly solar irradiance and luminous efficacy, to predict the potential lighting energy saving for a side-lit room. Two lighting control algorithms of photoelectric switching (on/off) and photoelectric dimming (top-up) have been coded in the program. A simulation for a typical UK office room has been conducted and the results show that energy saving due to the sunlight dependent on the various factors such as orientation, control methods, building depth, glazing area and shading types, etc. This simple tool can be used for estimating the potential lighting energy saving of the windows with various shading devices at the early design stage.

Non-toxigenic Escherichia coli O157:H7 strain NCTC12900 causes attaching-effacing lesions and eae-dependent persistence in weaned sheep

Ruminants are regarded as a primary reservoir for Escherichia coli O157:H7, an important human pathogen. Intimin, encoded by the Locus of Enterocyte Effacement by E. coli O157:H7 organisms, has been cited as one bacterial mechanism of colonisation of the gastrointestinal tract. To confirm this and to test whether a non-toxigenic E. coli O157:H7 strain would colonise and persist in a sheep model, E. coli O157:H7 strain NCTC12900, that lacks Shiga toxin (stx) genes, was evaluated for use in a sheep model of persistence. Following oral inoculation of six-week-old sheep, persistent excretion of NCTC12900 was observed for up to 48 days. E. coli O157-associated attaching-effacing (AE) lesions were detected in the caecum and rectum of one six-week-old lamb, one day after inoculation. This is the first recorded observation of AE lesions in orally inoculated weaned sheep. Also, mean faecal excretion scores of NCTC12900 and an isogenic intimin (eae)-deficient mutant were determined from twenty-four six-week-old orally inoculated sheep. The eae mutant was cleared within 20 days and had lower mean excretion scores at all time points after day one post inoculation compared with the parental strain that was still being excreted at 48 days. Tissues were collected post mortem from animals selected at random from the study groups over the time course of the experiment. The eae mutant was detected in only 1/43 samples but the parental strain was recovered from 64/140 samples primarily from the large bowel although rumen, duodenum, jejunum, and ileum were culture positive especially from animals that were still excreting at and beyond 27 days after inoculation.

Endogenous cholinergic tone modulates spontaneous network level neuronal activity in primary cortical cultures grown on multi-electrode arrays

Background Cortical cultures grown long-term on multi-electrode arrays (MEAs) are frequently and extensively used as models of cortical networks in studies of neuronal firing activity, neuropharmacology, toxicology and mechanisms underlying synaptic plasticity. However, in contrast to the predominantly asynchronous neuronal firing activity exhibited by intact cortex, electrophysiological activity of mature cortical cultures is dominated by spontaneous epileptiform-like global burst events which hinders their effective use in network-level studies, particularly for neurally-controlled animat (‘artificial animal’) applications. Thus, the identification of culture features that can be exploited to produce neuronal activity more representative of that seen in vivo could increase the utility and relevance of studies that employ these preparations. Acetylcholine has a recognised neuromodulatory role affecting excitability, rhythmicity, plasticity and information flow in vivo although its endogenous production by cortical cultures and subsequent functional influence upon neuronal excitability remains unknown. Results Consequently, using MEA electrophysiological recording supported by immunohistochemical and RT-qPCR methods, we demonstrate for the first time, the presence of intrinsic cholinergic neurons and significant, endogenous cholinergic tone in cortical cultures with a characterisation of the muscarinic and nicotinic components that underlie modulation of spontaneous neuronal activity. We found that tonic muscarinic ACh receptor (mAChR) activation affects global excitability and burst event regularity in a culture age-dependent manner whilst, in contrast, tonic nicotinic ACh receptor (nAChR) activation can modulate burst duration and the proportion of spikes occurring within bursts in a spatio-temporal fashion. Conclusions We suggest that the presence of significant endogenous cholinergic tone in cortical cultures and the comparability of its modulatory effects to those seen in intact brain tissues support emerging, exploitable commonalities between in vivo and in vitro preparations. We conclude that experimental manipulation of endogenous cholinergic tone could offer a novel opportunity to improve the use of cortical cultures for studies of network-level mechanisms in a manner that remains largely consistent with its functional role.

Land use intensity and trees on farms in Malawi

Rapidly increasing population densities in Malawi have put a huge strain on the existing agricultural land and the surrounding woodland. Smallholder agriculture is the dominant economic activity of Malawi’s rural population and many farmers have been forced to cultivate marginal lands with less fertile soils, making conditions much more difficult to grow crops. Natural woodland is under increasing pressure from the opening of new lands for cultivation and the increased demand for firewood, timber and other woody resources, with rural households historically obtaining most of their complementary inputs and saleable commodities from nearby areas of forest (Arnold, 1997a). Despite this increasing pressure, woodlands are not being cleared indiscriminately; selected indigenous species are left standing in fields and around households. These are joined by exotic species that are planted and maintained. These trees provide products and services that are vital, yielding food, firewood, building materials and medicine, replenishing soil fertility and protecting against soil erosion. Following a Boserupian approach, this study attempts to establish the reality of a trajectory of enhanced on-farm tree planting and management as population pressure mounts and as part of a more general process of agricultural intensification. The study examines the combination of factors (social, economic, political and environmental) that either stimulate or discourage on-farm tree planting on smallholdings in Malawi, highlighting how woodland resource use changes over a gradient of land use intensity. This study gives a detailed insight into the way that tree planting and management in the smallholder farming system in Malawi works and identifies a trend of increased tree planting/management alongside an increase in agricultural intensification. However, there is no single ‘path’ of intensification; the link between agricultural change and tree planting is complex and there are many trajectories of intensification that a farmer may follow, dependent on his/her social or economic circumstances. The study recommends that agroforestry interventions give rigorous consideration to the needs of the local community, and the suitability of trees to address those needs, before embarking on programmes that advocate tree planting and management as a panacea.

Content validation for level of use of feature rich systems: a Delphi study of electronic medical records systems

Introduction. Feature usage is a pre-requisite to realising the benefits of investments in feature rich systems. We propose that conceptualising the dependent variable 'system use' as 'level of use' and specifying it as a formative construct has greater value for measuring the post-adoption use of feature rich systems. We then validate the content of the construct as a first step in developing a research instrument to measure it. The context of our study is the post-adoption use of electronic medical records (EMR) by primary care physicians. Method. Initially, a literature review of the empirical context defines the scope based on prior studies. Having identified core features from the literature, they are further refined with the help of experts in a consensus seeking process that follows the Delphi technique. Results.The methodology was successfully applied to EMRs, which were selected as an example of feature rich systems. A review of EMR usage and regulatory standards provided the feature input for the first round of the Delphi process. A panel of experts then reached consensus after four rounds, identifying ten task-based features that would be indicators of level of use. Conclusions. To study why some users deploy more advanced features than others, theories of post-adoption require a rich formative dependent variable that measures level of use. We have demonstrated that a context sensitive literature review followed by refinement through a consensus seeking process is a suitable methodology to validate the content of this dependent variable. This is the first step of instrument development prior to statistical confirmation with a larger sample.

PERSiST: a flexible rainfall-runoff modelling toolkit for use with the INCA family of models

Runoff generation processes and pathways vary widely between catchments. Credible simulations of solute and pollutant transport in surface waters are dependent on models which facilitate appropriate, catchment-specific representations of perceptual models of the runoff generation process. Here, we present a flexible, semi-distributed landscape-scale rainfall-runoff modelling toolkit suitable for simulating a broad range of user-specified perceptual models of runoff generation and stream flow occurring in different climatic regions and landscape types. PERSiST (the Precipitation, Evapotranspiration and Runoff Simulator for Solute Transport) is designed for simulating present-day hydrology; projecting possible future effects of climate or land use change on runoff and catchment water storage; and generating hydrologic inputs for the Integrated Catchments (INCA) family of models. PERSiST has limited data requirements and is calibrated using observed time series of precipitation, air temperature and runoff at one or more points in a river network. Here, we apply PERSiST to the river Thames in the UK and describe a Monte Carlo tool for model calibration, sensitivity and uncertainty analysis

The interpretation and use of biases in decadal climate predictions

Decadal climate predictions exhibit large biases, which are often subtracted and forgotten. However, understanding the causes of bias is essential to guide efforts to improve prediction systems, and may offer additional benefits. Here the origins of biases in decadal predictions are investigated, including whether analysis of these biases might provide useful information. The focus is especially on the lead-time-dependent bias tendency. A “toy” model of a prediction system is initially developed and used to show that there are several distinct contributions to bias tendency. Contributions from sampling of internal variability and a start-time-dependent forcing bias can be estimated and removed to obtain a much improved estimate of the true bias tendency, which can provide information about errors in the underlying model and/or errors in the specification of forcings. It is argued that the true bias tendency, not the total bias tendency, should be used to adjust decadal forecasts. The methods developed are applied to decadal hindcasts of global mean temperature made using the Hadley Centre Coupled Model, version 3 (HadCM3), climate model, and it is found that this model exhibits a small positive bias tendency in the ensemble mean. When considering different model versions, it is shown that the true bias tendency is very highly correlated with both the transient climate response (TCR) and non–greenhouse gas forcing trends, and can therefore be used to obtain observationally constrained estimates of these relevant physical quantities.

Density of insect-pollinated grassland plants decreases with increasing surrounding land-use intensity

Pollinator declines have raised concerns about the persistence of plant species that depend on insect pollination, in particular by bees, for their reproduction. The impact of pollinator declines remains unknown for species-rich plant communities found in temperate seminatural grasslands. We investigated effects of land-use intensity in the surrounding landscape on the distribution of plant traits related to insect pollination in 239 European seminatural grasslands. Increasing arable land use in the surrounding landscape consistently reduced the density of plants depending on bee and insect pollination. Similarly, the relative abundance of bee-pollination-dependent plants increased with higher proportions of non-arable agricultural land (e.g. permanent grassland). This was paralleled by an overall increase in bee abundance and diversity. By isolating the impact of the surrounding landscape from effects of local habitat quality, we show for the first time that grassland plants dependent on insect pollination are particularly susceptible to increasing land-use intensity in the landscape.

Temperature-dependent orientational ordering on a spherical surface modeled with a lattice spin model

We study the orientational ordering on the surface of a sphere using Monte Carlo and Brownian dynamics simulations of rods interacting with an anisotropic potential. We restrict the orientations to the local tangent plane of the spherical surface and fix the position of each rod to be at a discrete point on the spherical surface. On the surface of a sphere, orientational ordering cannot be perfectly nematic due to the inevitable presence of defects. We find that the ground state of four +1/2 point defects is stable across a broad range of temperatures. We investigate the transition from disordered to ordered phase by decreasing the temperature and find a very smooth transition. We use fluctuations of the local directors to estimate the Frank elastic constant on the surface of a sphere and compare it to the planar case. We observe subdiffusive behavior in the mean square displacement of the defect cores and estimate their diffusion constants.

Phospholipid-based microemulsions suitable for use in foods

The preparation of nonaqueous microemulsions using food-acceptable components is reported. The effect of oil on the formation of microemulsions stabilized by lecithin (Epikuron 200) and containing propylene glycol as immiscible solvent was investigated. When the triglycerides were used as oil, three types of phase behavior were noted, namely, a two-phase cloudy region (occurring at low lecithin concentrations), a liquid crystalline (LC) phase (occurring at high surfactant and low oil concentrations), and a clear monophasic microemulsion region. The extent of this clear one-phase region was found to be dependent upon the molecular volume of the oil being solubilized. Large molecular volume oils, such as soybean and sunflower oils, produced a small microemulsion region, whereas the smallest molecular volume triglyceride, tributyrin, produced a large, clear monophasic region. Use of the ethyl ester, ethyl oleate, as oil produced a clear, monophasic region of a size comparable to that seen with tributyrin. Substitution of some of the propylene glycol with water greatly reduced the extent of the clear one-phase region and increased the extent of the liquid crystalline region. In contrast, ethanol enhanced the clear, monophasic region by decreasing the LC phase. Replacement of some of the lecithin with the micelle-forming nonionic surfactant Tween 80 to produce mixed lecithin/Tween 80 mixtures of weight ratios (Km) 1:2 and 1:3 did not significantly alter the phase behavior, although there was a marginal increase in the area of the two-phase, cloudy region of the phase diagram. The use of the lower phosphatidylcholine content lecithin, Epikuron 170, in place of Epikuron 200 resulted in a reduction in the LC region for all of the systems investigated. In conclusion, these studies show that it is possible to prepare one-phase, clear lecithin-based microemulsions over a wide range of compositions using components that are food-acceptable.

Modeling plant transpiration under limited soil water: comparison of different plant and soil hydraulic parameterizations and preliminary implications for their use in land surface models

Accurate estimates of how soil water stress affects plant transpiration are crucial for reliable land surface model (LSM) predictions. Current LSMs generally use a water stress factor, β, dependent on soil moisture content, θ, that ranges linearly between β = 1 for unstressed vegetation and β = 0 when wilting point is reached. This paper explores the feasibility of replacing the current approach with equations that use soil water potential as their independent variable, or with a set of equations that involve hydraulic and chemical signaling, thereby ensuring feedbacks between the entire soil–root–xylem–leaf system. A comparison with the original linear θ-based water stress parameterization, and with its improved curvi-linear version, was conducted. Assessment of model suitability was focused on their ability to simulate the correct (as derived from experimental data) curve shape of relative transpiration versus fraction of transpirable soil water. We used model sensitivity analyses under progressive soil drying conditions, employing two commonly used approaches to calculate water retention and hydraulic conductivity curves. Furthermore, for each of these hydraulic parameterizations we used two different parameter sets, for 3 soil texture types; a total of 12 soil hydraulic permutations. Results showed that the resulting transpiration reduction functions (TRFs) varied considerably among the models. The fact that soil hydraulic conductivity played a major role in the model that involved hydraulic and chemical signaling led to unrealistic values of β, and hence TRF, for many soil hydraulic parameter sets. However, this model is much better equipped to simulate the behavior of different plant species. Based on these findings, we only recommend implementation of this approach into LSMs if great care with choice of soil hydraulic parameters is taken

Temperature and oxygen dependent metabolite utilization by Salmonella enterica Serovars Derby and Mbandaka

Salmonella enterica is a zoonotic pathogen of clinical and veterinary significance, with over 2500 serovars. In previous work we compared two serovars displaying host associations inferred from isolation statistics. Here, to validate genome sequence data and to expand on the role of environmental metabolite constitution in host range determination we use a phenotypic microarray approach to assess the ability of these serovars to metabolise ~500 substrates at 25°C with oxygen (aerobic conditions) to represent the ex vivo environment and at 37°C with and without oxygen (aerobic/anaerobic conditions) to represent the in vivo environment. A total of 26 substrates elicited a significant difference in the rate of metabolism of which only one, D-galactonic acid-g-lactone, could be explained by the presence (S. Mbandaka) or the absence (S. Derby) of metabolic genes. We find that S. Mbandaka respires more efficiently at ambient temperatures and under aerobic conditions on 18 substrates including: glucosominic acid, saccharic acid, trehalose, fumaric acid, maltotriose, N-acetyl-D-glucosamine, N-acetyl-beta-D-mannosamine, fucose, L-serine and dihydroxy-acetone; whereas S. Derby is more metabolically competent anaerobically at 37°C for dipeptides, glutamine-glutamine, alanine-lysine, asparagine-glutamine and nitrogen sources glycine and nitrite. We conclude that the specific phenotype cannot be reliably predicted from the presence of metabolic genes directly relating to the metabolic pathways under study.